PLINK is a widely used open-source software tool for genome-wide association studies (GWAS) and population genetics analysis. It is designed to efficiently handle large datasets and offers a comprehensive suite of tools for analyzing genetic data.

Below is a simple guide on how to install and use PLINK in a Windows command-line (CMD) environment.

Installation Steps:

  1. Download PLINK: Visit the official PLINK website at https://www.cog-genomics.org/plink/ and download the version compatible with the Windows 64-bit operating system.

  2. Extract the Files: Locate the downloaded file, typically named plink_win64_20241022.zip, and extract its contents to a folder of your choice. For example, you can extract it to: E:\Mendelian Randomization\PRS score\plink_win64_20241022.(You can choose any folder path you prefer.)

  1. Set the PATH Environment Variable: Open the Windows Command Prompt (CMD) and run the following command:

“set PATH=E:\Mendelian Randomization\PRS score\plink_win64_20241022;%PATH%”

Press Enter. This command adds the directory containing plink.exe to your system’s PATH environment variable, allowing you to run PLINK from any location without specifying its full path each time.

4.Verify the Installation:

Type plink in the Command Prompt and press Enter. If the installation is successful, you will see the PLINK interface displayed, as shown below:

This confirms that PLINK has been successfully installed on your Windows system.

For example, in polygenic risk score analyses, we can use the following code to perform quality control (QC) on the target dataset.

plink --bfile EUR --maf 0.01 --hwe 1e-6 --geno 0.01 --mind 0.01 -write-snplist --make-just-fam --out EUR.QC
plink --bfile EUR --keep EUR.QC.fam --extract EUR.QC.snplist --indep-pairwise 200 50 0.25 --out EUR.QC
plink --bfile EUR --extract EUR.QC.prune.in --keep EUR.QC.fam --het --out EUR.QC